Blender for the chemical structure visualization
I'm very confident you can achieve what you want using Blender. Searching the web for "Blender for chemistry" gives you a number of hits including video tutorials and images what others did. Maybe this blog post is interesting for you:

https://patrickfuller.github.io/molecules-from-smiles-molfiles-in-blender/

Furthermore I found an addon for PDB import/export:

https://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB